beta.evenness: Beta diversity evenness (Taxon, Phylogenetic or Functional...

In BAT: Biodiversity Assessment Tools

Beta diversity evenness (Taxon, Phylogenetic or Functional Diversity - TD, PD, FD).

Description

Difference of evenness between pairs of sites.

Usage

beta.evenness(
  comm,
  tree,
  distance,
  method = "expected",
  func = "camargo",
  abund = TRUE
)

Arguments

comm	A sites x species matrix, with either abundance or incidence data.
tree	A phylo or hclust object (used only for PD or FD) or alternatively a species x traits matrix or data.frame to build a functional tree.
distance	A dist or matrix object representing the phylogenetic or functional distance between species. If both tree and distance are missing, taxonomic evenness is calculated.
method	Calculate evenness using "expected" values (default) or values based on "contribution" of species to the tree.
func	Calculate evenness using "Camargo" (default) or "Bulla" index.
abund	A boolean (T/F) indicating whether evenness should be calculated using abundance data.

Details

This measure is simply the pairwise difference of evenness calculated based on the index of Camargo (1993) or Bulla (1994) using the values of both species abundances and edge lengths in the tree (if PD/FD).

If no tree or distance is provided the result is the original index.

Value

Distance matrix between sites.

References

Bulla, L. (1994) An index of evenness and its associated diversity measure. Oikos, 70: 167-171.

Camargo, J.A. (1993) Must dominance increase with the number of subordinate species in competitive interactions? Journal of Theoretical Biology, 161: 537-542.

Examples

comm <- matrix(c(1,2,0,0,0,1,1,0,0,0,0,2,2,0,0,1,1,1,1,100), nrow = 4, byrow = TRUE)
distance <- dist(c(1:5), method = "euclidean")
tree <- hclust(distance, method = "average")
beta.evenness(comm)
beta.evenness(comm, tree)
beta.evenness(comm, tree, method = "contribution")
beta.evenness(comm, tree, abund = FALSE)

BAT documentation built on May 29, 2024, 7:35 a.m.